Locus 2251

Sequence ID	dm3.chr2L
Location	17,313,536 – 17,313,626
Length	90
Max. P	0.972593

overview

Window 2

Location	17,313,536 – 17,313,626
Length	90
Sequences	8
Columns	96
Reading direction	forward
Mean pairwise identity	67.64
Shannon entropy	0.65592
G+C content	0.42798
Mean single sequence MFE	-21.48
Consensus MFE	-9.45
Energy contribution	-10.31
Covariance contribution	0.86
Combinations/Pair	1.43
Mean z-score	-1.75
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.87
SVM RNA-class probability	0.972593
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17313536 90 + 23011544
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGCCAUAUAUGUAUGUAGCUACUGCAGCAGGGAACAUCAAUUUUGUUUCCCUCCGCCC------
..(((.((((((.....))))))...(((((((((((((....))))..((....)).))))))))).)))...................------ ( -26.00, z-score =  -2.65, R)
>droSim1.chr2L 17011893 90 + 22036055
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGCCAUAUAUGUGUGUAGCUACUGCAGCAGGGAGCAUCAAUUUUGUUUCCCUCCGCCC------
..(((.((((((.....))))))...(((((((((((((....))))..((....)).))))))))).)))...................------ ( -26.00, z-score =  -1.98, R)
>droYak2.chr2R 17345785 82 - 21139217
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGCCAUACA--------GCUACUGCAGCAGGGAGCAUCAAUUUUGUUCCCCUUCACCC------
..((((..(((...(((((((...........)))))))..--------((....)).)))(((((((.......))))))).))))...------ ( -23.50, z-score =  -2.30, R)
>droEre2.scaffold_4845 15650476 80 - 22589142
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGCCAUAUA--------GCUACUGCAGCAGGUAGCAUCAAUUUUGUUCCCCCGCCC--------
((..((((((..(((((((((...........)))))))))--------((((((......))))))..))))))..)).........-------- ( -23.20, z-score =  -2.81, R)
>droSec1.super_7 947396 86 + 3727775
AAUAAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGUCAUAUAUGUGUGUAGCUACUGCAGCAGGCAGCAUCAAUUUUGUUUCCGCCC----------
((((((((((..(((((((((...........)))))))))(((.(((.((....)).))).)))....)))))))))).......---------- ( -21.60, z-score =  -1.24, R)
>droAna3.scaffold_12916 12627585 86 - 16180835
AAUGAAAUUGCCUAUGCGGCAAUAUAGUUUCCUGGCCCA----------GCUCCUGCGGCAGGAGAGAAUCUUUUUAUUUUUUUCUGAGCCUGGUU
......((((((.....)))))).......((.(((((.----------((....))))(((((((((((......))))))))))).))).)).. ( -24.90, z-score =  -0.95, R)
>droPer1.super_68 133275 85 - 338515
AAUGAAACUGCCUAUGUGGCAAUAUAGUUUCCUGCCUCGGCUCCUCG--GCCGCUUCCCCUCUCCCUUCCUUUUUUGGUUUCCAUUC---------
...(((((((((.....))).................(((((....)--)))).......................)))))).....--------- ( -16.10, z-score =  -1.34, R)
>droWil1.scaffold_180703 791966 83 + 3946847
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUUACUUCUUCUACACUAA-AUUUGUUCCGACAUUUAUUAUGGUUUACCUUUACCU------------
((((((((((((.....))))))........................-...(((....)))))))))..(((........))).------------ ( -10.50, z-score =  -0.73, R)
>consensus
AAUGAAAUUGCCUAUGUGGCAAUAUAGUUUCCUGCCAUAUAU____G__GCUACUGCAGCAGGGAGCAUCAAUUUUGUUUCCCUCCGC________
......((((((.....))))))...(((.(((((.......................))))).)))............................. ( -9.45 = -10.31 +   0.86)

alignment

secondary structure

dotplot

Window 3

Location	17,313,536 – 17,313,626
Length	90
Sequences	8
Columns	96
Reading direction	reverse
Mean pairwise identity	67.64
Shannon entropy	0.65592
G+C content	0.42798
Mean single sequence MFE	-21.13
Consensus MFE	-9.51
Energy contribution	-9.96
Covariance contribution	0.45
Combinations/Pair	1.42
Mean z-score	-1.17
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.83
SVM RNA-class probability	0.829280
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17313536 90 - 23011544
------GGGCGGAGGGAAACAAAAUUGAUGUUCCCUGCUGCAGUAGCUACAUACAUAUAUGGCAGGAAACUAUAUUGCCACAUAGGCAAUUUCAUU
------..((((((((((.((.......)))))))).))))....((((.((....)).))))((....))..((((((.....))))))...... ( -25.70, z-score =  -2.09, R)
>droSim1.chr2L 17011893 90 - 22036055
------GGGCGGAGGGAAACAAAAUUGAUGCUCCCUGCUGCAGUAGCUACACACAUAUAUGGCAGGAAACUAUAUUGCCACAUAGGCAAUUUCAUU
------..(((((((((..............))))).))))....((((..........))))((....))..((((((.....))))))...... ( -22.84, z-score =  -0.95, R)
>droYak2.chr2R 17345785 82 + 21139217
------GGGUGAAGGGGAACAAAAUUGAUGCUCCCUGCUGCAGUAGC--------UGUAUGGCAGGAAACUAUAUUGCCACAUAGGCAAUUUCAUU
------.(((((((((((.((.......)).)))))(((((((...)--------)))..)))((....))..((((((.....)))))))))))) ( -22.60, z-score =  -0.54, R)
>droEre2.scaffold_4845 15650476 80 + 22589142
--------GGGCGGGGGAACAAAAUUGAUGCUACCUGCUGCAGUAGC--------UAUAUGGCAGGAAACUAUAUUGCCACAUAGGCAAUUUCAUU
--------.((((((((..((....))...)).))))))......((--------(....)))((....))..((((((.....))))))...... ( -19.50, z-score =  -0.32, R)
>droSec1.super_7 947396 86 - 3727775
----------GGGCGGAAACAAAAUUGAUGCUGCCUGCUGCAGUAGCUACACACAUAUAUGACAGGAAACUAUAUUGCCACAUAGGCAAUUUUAUU
----------.((((....)........((((((.....)))))))))...............((....))..((((((.....))))))...... ( -21.00, z-score =  -1.54, R)
>droAna3.scaffold_12916 12627585 86 + 16180835
AACCAGGCUCAGAAAAAAAUAAAAAGAUUCUCUCCUGCCGCAGGAGC----------UGGGCCAGGAAACUAUAUUGCCGCAUAGGCAAUUUCAUU
.....(((((((...................((((((...)))))))----------))))))((....))..((((((.....))))))...... ( -26.70, z-score =  -2.40, R)
>droPer1.super_68 133275 85 + 338515
---------GAAUGGAAACCAAAAAAGGAAGGGAGAGGGGAAGCGGC--CGAGGAGCCGAGGCAGGAAACUAUAUUGCCACAUAGGCAGUUUCAUU
---------.........((......))...........(((((.((--(..(....)..)))((....))....((((.....)))))))))... ( -20.00, z-score =  -1.23, R)
>droWil1.scaffold_180703 791966 83 - 3946847
------------AGGUAAAGGUAAACCAUAAUAAAUGUCGGAACAAAU-UUAGUGUAGAAGAAGUAAAACUAUAUUGCCACAUAGGCAAUUUCAUU
------------.(((........)))............((((.....-..(((((((...........)))))))(((.....)))..))))... ( -10.70, z-score =  -0.26, R)
>consensus
________GCGGAGGGAAACAAAAUUGAUGCUCCCUGCUGCAGUAGC__C____AUAUAUGGCAGGAAACUAUAUUGCCACAUAGGCAAUUUCAUU
.................................((((((.....................)))))).......((((((.....))))))...... ( -9.51 =  -9.96 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:47:43 2011